Avengers With A Twist
by MarvelAvengersFan2012
Summary: What if, during the battle in New York, a new character (or characters?) were thrown into the mix? I know, summary is very bad, but I hope you read, and I hope you enjoy. I know the title is very bad... sorry. Rated T because of paranoia. I DO NOT OWN AVENGERS.
1. Chapter 1

**Well, I have tons of Avengers stories that I have started but never finished (and don't know if I will…). This is one I decided to try posting on here. Hope you enjoy this chap and leave me comments, though please, nothing too harsh, okay?**

** Also, I do NOT, I repeat, DO NOT own Avengers (belongs to Marvel). Logan belongs to my friend. **

** Anyway, here is chapter one. I tried to write this according to the movie storyline, and I did the best that I could. If I made any mistakes, sorry. I also added my own little twists, I think. XD**

** Hope you enjoy!**

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"_All personnel, the evacuation order has been confirmed. Proceed to your designated vehicles for on campus evacuation. This is not a drill. Emergency personnel, proceed to your designated vehicles for on campus evacuation."_

In the midst of the evacuation of a S.H.I.E.L.D. research facility, agent Phil Coulson stood nearby a helipad as a helicopter descended upon it, silent and eyes hidden behind dark shades. As soon as the helicopter landed, a door opened and out stepped a woman with dark hair in a bun and wearing a dark blue S.H.I.E.L.D. uniform, fellow agent Maria Hill. Right behind her came another figure dressed in all black, complete with a long black coat, and had an eye patch over his left eye; Colonel Nick Fury, director of S.H.I.E.L.D. Fury and Hill walked over to where Coulson stood waiting.

"How bad is it?" Fury asked Coulson.

"That's the problem, sir." Coulson replied, taking off his shades. "We don't know."

Later they were walking through the facility where people were carrying different objects, transporting them. Coulson further explained the situation to the director.

"Dr. Selvig read an energy surge from the Tesseract four hours ago," he said.

"NASA didn't authorize Selvig to go to test phase," Director Fury replied, raising the eye brow on his good eye.

"He wasn't testing it," Coulson said. "He wasn't even in the room. Spontaneous event."

"It just turned itself on?" Agent Maria Hill questioned from behind them.

"Where are the energy levels now?" Fury asked Coulson.

"Climbing," Phil answered. "When Selvig couldn't shut it down, we ordered the evac."

Fury processed this. "How long to get everyone out?"

"The campus should be clear in the next half hour," Coulson told him.

"Do better," Fury said shortly; Phil nodded and walked away.

Fury and Hill reached a flight of stairs and began descending them. Hill thought over everything she had heard, and then spoke up.

"Sir, evacuation may be futile," Hill told Fury as they descended the stairs.

"We should tell them to go back to sleep?" Fury answered without looking at her.

"If we can't control the Tesseract's energy, there may not _be_ a minimum safe distance," Hill said after they reached the bottom of the stairs and were walking through a lower level of the facility, Fury heading for a lab.

"I need you to make sure that the Phase Two prototypes are shipped out," Fury said, not answering her comment.

"Sir, is that really a priority right now?" Hill asked and stopped at the bottom of a short flight of stairs that Fury climbed up.

Fury turned around to look at her. "Until such time as the world ends we will act as though it intends to spin on. Clear out the tech below. I want every piece of Phase Two on a truck, and gone."

"Yes sir," Hill answered as she walked past the director and signaled at two armed agents standing nearby. "With me."

Later, Fury entered into a large lab where the Tesseract was being held/monitored, and where scientists were running tests and scans on it. "Talk to me, doctor."

Eric Selvig looked up at the sound of Fury's voice. "Director," he said, coming out from behind from where the Tesseract was being held on a platform, and walking toward Fury.

"Is there anything we know for certain?" Fury inquired.

"The Tesseract is misbehaving," Selvig replied, while in the background, a scientist poked a probe at the icy blue cube, causing it to spit out small bolts of bright blue energy.

"Is that supposed to be funny?" Fury asked, raising an eyebrow.

"No, it's not funny at all," Selvig replied, reaching the director, then beginning to walk beside him as the two made their way back to the location where Selvig had come from moments before. "The Tesseract's not only active, she's… behaving."

"I assume you pulled the plug?" Fury said in response.

"She's an energy source," Selvig countered, worried. "We turn off the power she turns it back on. If she reaches peak level…"

"We were prepared for this doctor," Fury interrupted Selvig, who walked behind a monitor and examined the screen. "Harnessing energy from space."

"We don't have the harness," Selvig countered again, looking up from the monitor. "My calculations are far from complete. She's throwing off interference, radiation… nothing harmful, low levels of gamma radiation."

Fury, who had looked at the Tesseract while Selvig was speaking, looked back at him. "That can be harmful. Where are Agent Barton and his sister?"

"The Hawk?" Selvig snorted. "Up in his nest, as usual." He gestured to a high balcony overhead. "As for Logan, she's around here somewhere. There's no telling."

"Agents, report," Fury spoke into his earpiece, and on the high overhead balcony, Clint Barton stood from where he had been crouching, immediately got up and clipped a latch on his belt to a rope nearby, sliding down it. His sister Logan, a shapeshifter with a couple of different forms, who was in her griffin form nearby, extended her wings and flew down to meet Fury, transforming back into human form after she landed.

"I gave you two this detail so you could keep a close eye on things," Fury told the two sternly as the three of them walked toward the platform the Tesseract was on.

"Well, I see better from a distance," Clint replied as they walked.

"As do I," Logan chimed in. "When I am in my griffin form, at least."

"Well, have you two seen anything that might set this off?" Fury asked the brother and sister.

"Doctor, it's spiking again," A female scientist called to Selvig from behind a monitor.

"No one's come or gone," Clint told Fury as they and Logan stepped up onto the Tesseract platform. "Selvig's clean, no contacts, no IMs…. If there was any tampering sir, it wasn't from this end."

Fury looked at him. "At this end?"

"Yeah, the cube is a doorway to the other end of space, right?" Logan chimed in, looking at Fury herself. "Door's open from both sides."

Suddenly the cube began to pulse brighter and brighter, throwing out larger bolts of energy, causing Logan, Clint, and Fury to look at it, startled. The three hurriedly backed off the platform and away a bit. The whole room shook and then suddenly, a large beam of blue energy shot from the cube, hitting the wall opposite it as those in the room looked on in shock. A large portal opened and moments later, there was an explosion. Fury, Clint, and Logan covered their faces as blue light shot out, and lowered their hands when the blue glow died down. They looked toward the platform and got the shock of their lives as the saw what, or rather who, was now there.

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**That's the end of Chapter 1! Tell me your thoughts, but please, nothing too harsh. If you're wondering, Logan (whose last name is obviously Barton; she's Clint's sister) is a friend of mine's OC, whose is also a user on (AvengersHawkeyeLover is her pen name). If you're wondering whether I have an OC in this, you will just have to wait and see! :D**

** Until next chapter,**

** MarvelAvengersFan2012**


	2. Chapter 2

** Okay, so I know I haven't updated for a while, and I'm sorry. Finally, here is chapter 2, and I hope you enjoy it. I have been using the movie as a reference to help, and also, I have gotten inspirations from other works, and if this chap offends anyone, please tell me ASAP.**

** I have also had some help from a fellow fanfic user, Ophelia Lokisdottir, please check out what she posted, and a friend of mine, who is yet another fanfic user (AvengersHawkeyeLover). **

** I DO NOT OWN ANY PART OF THE AVENGERS MOVIE (ANY AT ALL), OR AVENGERS IN GENERAL. THAT BELONGS TO MARVEL. I also do not own the character Logan, that OC belongs to my friend. **

** Enjoy (I hope)! :D**

X

Everyone in the room stared at the newcomer kneeling on the platform. It was a man with black hair that curved up towards the ends, wore a green and black outfit, and clutched a long golden spear with a curved end, a ball of eerie blue light glowing at the tip. He slowly looked up with a grin full of mischief, which he soon lost.

_"Okay, that dude seriously looks like he's destined to join the circus or something," _Logan thought to herself.

"Sir, please put down the spear!" Fury commanded the newcomer.

The man looked down at his spear, and then fired a blast of energy from it. Logan quickly transformed into a griffin and flew up high as her brother dove at Fury, pushing him out of the way. An armed agent immediately open fired on the newcomer, who furiously turned in his direction and leaped powerfully from his platform, landing on and nailing the agent with his spear. Two other armed agents fired at him behind; the man sharply turned around, throwing small knives at the two agents, hitting his targets.

The man fired more bolts of energy at the people in the room. Logan saw her brother and two other agents fire at him with their own guns. The man turned furiously on them, firing a bolt of energy that hit one of the agents behind him while the other and Logan's brother dove out of the way. Logan landed back on the ground and changed from a griffin back to human then over to cheetah. Once in her cheetah form, she made a rush at the newcomer, teeth bared in a vicious snarl. The man's head snapped around when he heard her coming. He jumped into the air just as Logan ran underneath him.

Logan skidded to a stop and turned around, prepared to charge the newcomer again. The newcomer gave her a beckoning gesture.

"Here kitty kitty," he taunted, smirking.

Logan gave an enraged growl rushed at him again. When she about reached his position, she lunged with snapping jaws. She was shocked to go right through him and his image faded. She knew at once it had been an illusion. So where was the newcomer?

She changed back to human form and looked around for the newcomer. First time around she didn't see him anywhere. Her brow furrowed, and she looked around again. All of sudden the black haired man was right up in front of her; reacting instantly she raised her fist and threw a mighty punch at him. The newcomer was even faster, effortlessly knocking her fist aside and then immediately he touched the tip of his spear to her chest.

Energy flowed from the tip of the spear and into Logan's chest. It flowed up towards her eyes, and inside her mind, it was like a war. Logan squeezed her eyes shut and tried her best to fight the energy that flowed into and invaded her mind, threatening to push her back and assume full control of her mind. She fought so hard that in mere seconds, intense pain was rippling throughout her mind.

"You have spirit, shapeshifter," Loki mused as he looked at Logan. "But sooner or later, you will see that trying to fight me is useless."

Meanwhile, Fury, who was inching his way closer to the Tesseract's chamber, saw what was happening to Logan and saw out of the corner of his good eye her brother Clint, who had struggled to his feet, clutch his head in pain while staggering back a couple of steps. The siblings had a mental link, which Fury had known about since before they came to work for him. Their link allowed them to feel what each other felt, so Fury knew right away that whatever was happening to Logan was causing her a great deal of pain.

"What is that man doing to her that causes her this much agony?" Fury thought angrily to himself.

The battle going on in Logan's mind was quickly becoming a losing one; her will, which had been so strong at the beginning, was beginning to weaken, and soon, she was ultimately defeated. She felt herself being pushed to a very deep corner of her mind and swiftly trapped there. From where she was trapped in her mind, Logan saw that her vision had become warped with a strange aqua blue tint.

The newcomer lowered his spear and smirked. "That's better. You will be a valuable asset in my plan."

"I know I will be," Logan answered in a lifeless tone of voice. "How may I serve you now?"

The newcomer paused for a moment, and then smiled evilly. "I think you know."

"Yes, sir, I do," Logan answered in the same lifeless tone. Inside her mind, Logan began to panic as she realized what was about to happen and as she felt her form start to change to that of a horse.

"No!" she mentally screamed. Her will all of a sudden came back stronger than ever, and she began to fight with all her might. The newcomer looked at her and saw her eyes flash from bright blue back to their original color of green. Her eyes closed and her head shook really hard before she suddenly stiffened as her mind was fully taken over again.

As Logan's form finished changing into a horse, her eyes opened, once more the bright blue of the Tesseract. Her icy blue gaze fixed on Clint, and she began to clop over to him.

Meanwhile, Clint shook his head as another stab of shooting pain in his head finally subsided. He looked up to see his sister Logan making her way over to him in her horse form. As he looked at her, he began to feel that something was up with her, so when Logan stopped some feet in front of him, he gave her a concerned look.

"Are you okay, LJ?" he asked her. The horse snorted in response, and that's when Clint noticed her eyes. As he stared at the icy blue color irises that showed no signs of emotion, he stepped back. "What's wrong, Logan?"

His sister didn't do anything in reply. Clint glanced over her shoulder and saw the newcomer swiftly making his over to them. Immediately he stiffened into a defense stance.

"LJ behind you!" he yelled out. The horse's head turned to look at the newcomer and nickered at him. The newcomer reached them and laid his hand on the horse's side. Clint stared in shock for a few moments, and then his expression became furious.

"What did you do to my sister?" he hissed, his hands curling into fists so tight that if he wasn't wearing gloves, others could see the veins standing out.

"Well, let's just say I've expanded her horizons," the newcomer countered smoothly, a smirk creeping into his voice.

"You're a maniac!" Clint yelled out, and then quickly whipped his gun out of his belt. Before he could even make a move, the newcomer grabbed his arm in a grip that Clint couldn't break; he struggled against the newcomers grasp.

"You have heart…" the newcomer purred almost thoughtfully, and without hesitation, touched the tip of his staff to Clint's chest.

X

The effect of the spear on Clint was much faster than it had been for Logan. Fury watched with an unfathomable expression as Clint stop struggling against the newcomer's grip and re-holster his gun, his eyes also now glowing the eerie blue of the spear. Still, he didn't hesitate to remove the Tesseract from where it previously had been sitting and carefully place it in a briefcase, unnoticed by the newcomer, that is, until Fury turned to quietly leave.

"Please don't," the newcomer called out, turning to look him. "I still need that."

"This doesn't have to get any messier," Fury said without turning around.

"Of course it does," the newcomer answered. "I've come too far for anything else. I am Loki, of Asgard, and I am burdened with glorious purpose."

"Loki!" Dr. Selvig said in shock as he stood up from the side of an unconscious scientist. "Brother of Thor!" Loki looked at him sharply at the mention of Thor's name.

"We have no quarrel with your people," Fury said to Loki, holding up a hand.

"An ant has no quarrel with a boot," Loki countered.

"You planning to step on us?" Fury asked as if he couldn't believe what he was hearing.

"I come with glad tidings," Loki answered, while walking over to stand near Selvig. "Of a world made free."

"Free from _what_?" Fury asked.

"Freedom. Freedom is life's great lie," Loki replied. "Once you accept that, in your heart…" He quickly turned to Selvig, placing the tip of the spear against his chest. "You will know peace."

"Yeah, you say peace," Fury said as he stared at Loki. "I kinda think you mean the other thing."

Meanwhile, Clint and Logan, who was now back in her human form, walked toward Loki after glancing upward at a portal above them all.

"Sir, Director Fury is stalling," Clint informed Loki.

"This place is about to blow and drop 100 feet of rock on us," Logan continued. "He means to bury us."

"Like the pharaohs of old," Fury said, looking at the two siblings.

"They're both right," Selvig cut in. "The portal is collapsing in on itself. We've got maybe two minutes before this goes critical."

"Well then," As soon as Loki said that, Clint whipped out his gun and shot Fury, who fell to the floor, losing hold of the briefcase. Clint quickly grabbed it and left the room with Loki, Logan, Selvig, and another possessed agent.

"We need these vehicles," Logan's brother gestured over to them when they walked into the garage. As they walked over to a larger truck, Agent Maria Hill, who was in the room, spotted them, her gaze falling to Loki. Inside her mind, Logan fought to call out to Maria to warn her about the newcomer Loki, but because of the spell that was over her, that simply was not going to happen.

Hill's brow furrowed. "Who's that?"

"He didn't tell me," Clint answered as he and the rest of the group went to get into the truck. Logan saw Maria gaze at them suspiciously, and then turn to walk away.

_"Hill!" _The frantic call coming through Hill's radio caused Loki, Clint, and Logan to all to look at her sharply. _"Do you copy?! The Bartons… have turned!"_

Hill's head snapped around, and all at once, Logan was forced to assume her cheetah form, and dive at Hill, teeth bared. Hill barely had enough time to roll out of the way before Logan's teeth snapped viciously in the exact spot where she'd been. Logan was horrified at how close she'd been to seriously wounding (or worse) Hill; that only added to her fury at Loki, which kept building.

Just as quickly as she was ordered to rush Hill, Logan was ordered back to back to the truck. With a quick, swift move, Logan jumped into the backseat and her brother closed the door behind her. As she settled herself on the seat, her brother quickly jumped into the truck as well, started the engine, and they sped away.

X

"We're clear upstairs, sir. We need to go." Phil Coulson's voice came through Fury's radio sometime later as the S.H.I.E.L.D. director exited the facility and quickly ran to a waiting chopper nearby. Without hesitation he took the chopper to the air, just as, inside, a devastating explosion of energy caused the entire facility to begin collapsing in on itself. Fury critically surveyed the scene with his good eye, the expression on his face that was half shock, half anger.

As his copter flew through the air away from the doomed facility, he passed over a tunnel that a truck came speeding out of. Fury peered at the truck through the window of the copter suspiciously, and no sooner did the driver of the truck notice the copter, did they veer off the main road and began racing through the desert. Fury himself immediately took action.

Fury slid open the copter door and raised his gun, opening fire at the truck. Then a bright blue blast of energy soared his way and struck the copter, and immediately it began plummeting towards the ground. Keeping a solid grip on his gun, Fury jumped clear of the copter just as it crashed, landing on its side and skidding some distance.

Fury rose up off the ground onto one knee and fired more shots at the truck, but by then, it was too far away. He lowered his gun and stood up, watching it disappear into the horizon.

_"Director. Director Fury, do you copy?" _Coulson's voice came through Fury's radio, which he immediately grabbed.

"The Tesseract is with a hostile force. I have men down. Hill?"

_"A lot of men still under, don't know how many survivors," _came Hill's reply.

"Sound a general call," Fury ordered her. "I want every living soul not working rescue looking for that briefcase."

_"Roger that." _Hill answered.

"Coulson, get back to base. This is a Level Seven," Fury went on, and his voice picked up a different tone. "As of right now, we are at war."

_"What do we do?" _Coulson asked.

He lowered his radio and stared into the distance once more, deep in thought, and suddenly, he knew just what he had to do.

X

**I hoped you liked this chap, and reviews are appreciated (plz no flames though), and like I said, if this chap offends ANYONE, please let me know. I will try to have chap 3 up before long.**

** Until next time,**

** MarvelAvengersFan2012**


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